I'm one of the main developers of R Markdown. As @jcheng said, it is definitely not our intention to lock you in RStudio for any of our R packages. You probably

I'm one of the main developers of R Markdown. As @jcheng said, it is definitely not our intention to lock you in RStudio for any of our R packages. You probably can't imagine how hard I have been trying to avoid relying on RStudio specifically for certain features. There are decisions that I can definitely make in favor of the RStudio IDE, but usually I don't do that, and hope things also work well with other editors. Pretty much everything you do in the RStudio IDE for R Markdown documents or projects can be done in command line. It's not possible that a document is no longer reproducible just because you stop using RStudio.